I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether ...

In this question we are examining a bacterial RNA polymerase that elongates at 20 codons per second.
Question 1: How long will this RNA polymerase take to transcribe the Lac Z gene at 3510 base pairs?
...

For a little less than half the cell cycle, a significant number of genes are represented twice (just before dividing). Does the cell differentiate between these DNA in any way or are transcription ...

I was wondering if anybody knows some publication about macro lncRNA (very long unspliced RNAs) or more generally a transcribed RNA that may lead to cis-DNA looping of genomic regions overlapped by ...

I've heard a statement in a talk that U-rich sequences cause transcriptional pausing. The intuitive explanation for this was that the UTP concentration is lower in the cell than the ATP concentration. ...

Each DNA (RNA) sequence has 6 possible Open Reading Frames(ORF). My question is: What are the theoretical bases of in vitro or in silico tries to find correct reading frame of a sequence?
Is it just ...

Before anything else please pay attention of the double quotes on the "equal" in the title - I know they are not equal, but you will understand in a bit.
If I look at the DNA codon table here or in ...

I'm wondering if there are meant to be differences in DNA methylation between the forward and the reverse strand of the gene? I'm wondering because in primer design for bisulfite pyrosequencing one ...

According to this video (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions.
How are these micro-lesions ...

This article gives measurement of transcription rate and the unit they're using is microarray per hour.
For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page ...

Cooperativity in gene expression is an important feature of many regulatory networks. Described using the Hill function, the most common example is a transcription factor (TF) that when bound to its ...

I need to know the correct term(s) which are usually used in the parlance of both biology and bioinformatics for this study approach:
About 11 transcripts were investigated using qPCR for a number of ...

When transcription factors attach to the DNA strand - How do they know in which direction they have to initialize the transcription by rna polymerase? Is it always read in the same direction anyway? ...

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites).
The motifs belong to several species, and I wanted to cluster these ...

Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene:
One of the simplest ways to model GFP transcription is to use an ODE:
$\frac{d [GFP_{mRNA}]}{dt} = a - ...

I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it ...

My book keeps giving different indicators as to whether the promoters are on the coding or template strand.
It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that ...

I'm doing my High School biology final on Progeria, and am wondering what type of mutation causes this disease.
I know that the LMNA gene codes for the "prelamin A" protein, and that protein contains ...

I am making mRNA by in vitro transcription for transfection purposes. There is a lot of literature about how protein expression is increased and innate immune activation is decreased by substituting ...

If the sole known function of a gene is to activate a transcription factor, would that gene also be considered a transcription factor, or is there a word for such genes that are further upstream on ...

After looking at this question, some other questions poped in my mind.
The DNA code is redundant, there are 20 amino acids for 64 possible nucleotide combinations. Therefore some amino acid are coded ...

What is the trigger for DNA to produce proteins or RNA?
I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses ...

I have noticed that some TF binding sites are located in the introns of the genes.
I am puzzled about whether the TF only binds to DNA in the initiation stage of transcription and will detach during ...

Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (S. cerevisiae) and S. pombe genomes? Even if these are only de novo predictions, I would like ...

I've read this paper where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, Xanthomonas oryzae, and disrupt the hijacking of a gene network in the rice ...